How did you go about updating the firmware. There are usually lots of warnings and a step by step process. The manuals state quite clearly that the firmware leaves the charger disabled. Done right the update process asks you to save the settings file, update the firmware then reload the settings file.
Extract from the remote update manual, which probably explains why your batteries have not charged.
After the firmware update is completed, the inverter is switched on again. The settings will have been reset to their defaults. And, to prevent overcharging, all charge voltages have been set to the nominal battery voltage, being 12V, 24V or 48V. This effectively disables the charger.